A comprehensive dataset of 32 million pentapeptide structures for high-throughput virtual screening

This database contains a large-scale library of peptide conformers together with per-conformer quality annotations and an index that makes it easy to locate any conformer. This is an exhaustive set of all possible amino acid pentamers (3.2 million sequences) with 10 conformers per sequence, totaling 32 million peptide structures. Peptides are represented by folders named H_<sequence> (for example H_AAAAA), where sequence is the amino acid sequence used in downstream tables; each folder contains multiple conformers indexed by conformer number H_<sequence>_<conf_number>. The conformer coordinate data are distributed across Zstandard-compressed tar archives named by the first residue of the sequence, using one letter amino acid codes (for example A.tar.zst, C.tar.zst, E.tar.zst, etc). A peptide with Sequence = "AAAAA" is stored in A.tar.zst; a peptide with Sequence = "QWVDE" is stored in Q.tar.zst if present, otherwise in the archive matching the first residue of its sequence. Sequence_conformer_location.txt is the lookup table linking Sequence and Conformer to the corresponding folder name and archive location (the Location field), so you can programmatically jump from a row in your analysis tables to the compressed file that contains the structure. Conformer_metrics.txt contains per-conformer annotations, including Ramachandran classifications for the relevant residues (for example Favored, Allowed, Outlier, plus residue-type context), fields to indicate whether a matching structure exists in the PDB; when a match exists, it records the PDB entry identifier and the RMSD between the deposited conformer and the matched PDB structure, and the initial conformation used for chimeraX. To extract an archive on Windows: # Step 1: decompress the .zst to a .tar zstd -d A.tar.zst -o A.tar # Step 2: extract the tar tar -xf A.tar # Optional: delete the intermediate tar to save space Remove-Item A.tar You can repeat for any archive, for example C.tar.zst, G.tar.zst, etc. On Linux / macOS: zstd -dc A.tar.zst | tar -xf -